Egyptian Coptic priests react during the farewell of Pope Shenouda III, the head of Egypt's Coptic Orthodox Church during his funeral, in the Abassiya Cathedral in Cairo on Tuesday. Thousands of mourners dressed in black gathered in Cairo on Tuesday for the funeral of Pope Shenouda, who spent his final years trying to comfort a community disturbed by the rise of political Islam.

Cairo — Tens of thousands of people turned out for the funeral today of Pope Shenouda III, the man Egypt's Coptic Christians saw as not just a leader, but a protector and a father who defended his flock in hard times, from the presidency of Anwar Sadat to the fall of Mubarak. Many Christians are devastated that his death on Saturday came at such a difficult time for them.

“In the circumstances we are in now, we needed him more than ever,” says Mariem Seif, who stood amid the throngs outside St. Mark’s Cathedral in Cairo waiting to catch a glimpse of the car that would carry the pope’s body away. Ms. Seif begins to weep as she ticks off the recent instances of attacks against Christians – a church bombing over a year ago that killed nearly two dozen people; multiple churches burned over the last year; and in October, an Army attack on a Christian protest that left 27 dead and the Christian community traumatized.

“We were so angry,” says Seif. “But he was wise and calm, and calmed us down, to protect us.”

Shenouda began his tenure as leader of the Coptic Orthodox Church four decades ago at a time of rising sectarianism that made Egyptian Christians feel under threat. By the time his patriarchy ended this weekend, the Christian community was once again feeling vulnerable.

Like many, Seif is not convinced that the next pope will be able to fill Shenouda's shoes. In a measure of the devotion many Copts felt for Shenouda, tens of thousands of people came to the cathedral Sunday and Monday to catch a last glimpse of his body. They waited for hours, braving deadly stampedes. Three people died and more than 50 were wounded in the crush of the crowd. Today, some of those who could not get inside the cathedral waited outside, following the service via handheld radios pressed to their ears.

Banished by Sadat

When Shenouda became leader of the church in 1971, then-President Anwar Sadat was using Islamic rhetoric and encouraging Islamist groups in an attempt to boost his support. It was a stark change from the secularism of his predecessor, former President Gamal Abdel Nasser. Christians began to feel targeted.

When Shenouda challenged Sadat over this, Sadat banished the pope to a monastery – the same one where the pope will be buried today. Shenouda spent three years there. When he emerged at the invitation of the next president, Hosni Mubarak, he seemed to have found a new way of protecting his flock.

Instead of challenging Mr. Mubarak, he supported him. This gave the pope a position from which to negotiate with government officials on behalf of the church. And he was good at this, says Samia Sidhom, managing editor of the Coptic newspaper Al Watani. He also cultivated good relations with the top Muslim clerics in Egypt.

Rise of sectarianism

Yet toward the end of Mubarak's rule, sectarianism was once again on the rise. As attacks on Christians increased, the pope was placed in a difficult position: He depended on his closeness to Mubarak’s regime to win concessions on behalf of Christians, yet the regime was allowing and even perpetrating sectarianism and discrimination, angering Christians.

Copts became torn: they criticized Mubarak’s regime for not protecting them, but at the same time they considered him a bulwark against Islamic extremism. The uprising that forced Mubarak from power and ushered in an Islamist majority in parliament was for some, the realization of their worst fears.

On Monday, several salafi members of parliament left the chamber or remained seated while the rest of the members stood for a moment of silence to mourn the pope.

Pope oversaw Coptic expansion in US

Despite the politics he faced in Egypt, most Copts will remember the pope for his legacy within the church. He continued the renaissance of the church begun by his predecessor, Pope Kyrillos VI, who began building up and expanding church institutions. Shenouda continued that work, leading many Christians to become more involved in the church.

He held the conservative line as some petitioned for less church control over personal lives, particularly in the case of divorce. Yet his position of not granting divorces to Christians except in extreme circumstances was in line with what most Copts believed.

The pope did introduce some democratic practices in the church, says Ms. Sidhom. “For instance, he never ordained a priest unless the congregation nominated him,” she says. She calls his teaching lenient, calling for understanding and mercy. “He would always tell the priests and say out in public, 'Don't be too hard on the people. You have to understand their needs,’ ” says Sidhom.

Shenouda also oversaw an explosion of Coptic churches outside Egypt, including in the US.